<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div>Hi Christophe,</div>
<div><br>
</div>
<div>if you are passing the omero hostname directly to loadOmero() you are actually bypassing the</div>
<div>content of your ice.config file.</div>
<div><br>
</div>
<div>To pass both the hostname and custom properties, you can create a Java properties object i.e.</div>
<div><br>
</div>
<div>
<div style="margin: 0px; font-family: Menlo;"><font size="2">>> props = java.util.Properties();</font></div>
<div style="margin: 0px; font-family: Menlo;"><font size="2">>> props.setProperty('omero.host', hostname);</font></div>
<div style="margin: 0px; font-family: Menlo;"><font size="2">>> props.setProperty('Ice.MessageSizeMax', '10000000');</font></div>
</div>
<div style="margin: 0px; font-family: Menlo;"><font size="2">>> c = loadOmero(props);</font></div>
<div><br>
</div>
<div><br>
</div>
then you can check that your Ice.MessageSizeMax is properly configured client-side:
<div>
<div><br>
</div>
<div><font size="2"><span style="font-family: Menlo;">>> c.getProperty('</span><span style="font-family: Menlo;">Ice.MessageSizeMax')</span><span style="font-family: Menlo;">;</span></font></div>
<div><br>
</div>
<div>Sebastien</div>
<div><br>
<div>
<div>On 9 Feb 2015, at 16:18, Christophe TREFOIS <<a href="mailto:christophe.trefois@uni.lu">christophe.trefois@uni.lu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
I assumed it’s in KB. So I changed it locally but it still throws the error.
<div class=""><br class="">
</div>
<div class="">I just put ice.config in my working directory and use the normal loadOmero(om_host) to load the config.</div>
<div class=""><br class="">
</div>
<div class="">Since I still get the error, I assume I have to set it on the server?</div>
<div class=""><br class="">
</div>
<div class="">Is my image too big?</div>
<div class=""><br class="">
</div>
<div class="">Thanks,<br class="">
<div class="">
<meta name="format-detection" content="telephone=no" class="">
<p style="font-family: Arial, sans-serif; font-size: 10pt; line-height: 16px; color: rgb(33, 33, 33);" class="">
<span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">Dr Christophe Trefois, Dipl.-Ing.</span>
<span style="display: inline;" class=""></span><br class="">
<span style="color: rgb(61, 59, 59); display: inline; font-size:7.5pt;" class="">Technical Specialist / Post-Doc</span>
</p>
<p style="font-family: Arial, sans-serif; font-size: 7.5pt; line-height: 16px;" class="">
<span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">UNIVERSITÉ DU LUXEMBOURG</span><br class="">
<span style="display: inline;" class=""><br class="">
</span><span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">LUXEMBOURG CENTRE FOR SYSTEMS BIOMEIDINCE</span><br class="">
<span style="color: rgb(61, 59, 59); display: inline;" class="">Campus Belval | House of Biomedicine
<br class="">
7, avenue des Hauts-Fourneaux <br class="">
L-4362 Esch-sur-Alzette </span><br class="">
<span style="color: rgb(61, 59, 59); display: inline;" class="">T: </span><span style="color: rgb(61, 59, 59); display: inline;" class="">+352 46 66 44 6124</span>
<br class="">
<span style="color: rgb(61, 59, 59); display: inline;" class="">F: </span><span style="color: rgb(61, 59, 59); display: inline;" class="">+352 46 66 44 6949</span>
<span style="display: inline;" class=""><br class="">
</span><a href="http://www.uni.lu/lcsb" style="color: rgb(0, 109, 189); display: inline;" class="">http://www.uni.lu/lcsb</a>
</p>
<p style="font-family: Arial, sans-serif; font-size: 14px; line-height: 16px;" class="">
<a href="https://www.facebook.com/trefex" style="display: inline;" class=""><img width="24" height="24" data-filename="facebook.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/facebook.png" alt="Facebook" class=""></a>
<a href="https://twitter.com/Trefex" style="display: inline;" class=""><img width="24" height="24" data-filename="twitter.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/twitter.png" alt="Twitter" class=""></a>
<a href="https://plus.google.com/+ChristopheTrefois/" style="display: inline;" class="">
<img width="24" height="24" data-filename="googleplus.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/googleplus.png" alt="Google Plus" class=""></a>
<a href="https://www.linkedin.com/in/trefoischristophe" style="display: inline;" class="">
<img width="24" height="24" data-filename="linkedin.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/linkedin.png" alt="Linkedin" class=""></a>
<a href="http://skype:Trefex?call" style="display: inline;" class=""><img width="24" height="24" data-filename="skype.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/skype.png" alt="skype" class=""></a>
</p>
<div style="font-family: Arial, sans-serif; font-size: 14px; line-height: 16px;">
<br class="webkit-block-placeholder">
</div>
<p style="font-family: Arial, sans-serif; color: rgb(61, 59, 59); font-size: 9px; line-height: 16px;" class="">
----<br class="">
This message is confidential and may contain privileged information. <br class="">
It is intended for the named recipient only. <br class="">
If you receive it in error please notify me and permanently delete the original message and any copies.
<br class="">
----<br class="">
</p>
</div>
<br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 09 Feb 2015, at 14:47, Christophe TREFOIS <<a href="mailto:christophe.trefois@uni.lu" class="">christophe.trefois@uni.lu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Sébastien,
<div class=""><br class="">
</div>
<div class="">What is the unit?</div>
<div class=""><br class="">
</div>
<div class="">And, what’s the default on the server side?</div>
<div class=""><br class="">
</div>
<div class="">Thank you for your help,</div>
<div class=""><br class="">
<div class="">
<meta name="format-detection" content="telephone=no" class="">
<p style="font-family: Arial, sans-serif; font-size: 10pt; line-height: 16px; color: rgb(33, 33, 33);" class="">
<span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">Dr Christophe Trefois, Dipl.-Ing.</span>
<span style="display: inline;" class=""></span><br class="">
<span style="color: rgb(61, 59, 59); display: inline; font-size:7.5pt;" class="">Technical Specialist / Post-Doc</span>
</p>
<p style="font-family: Arial, sans-serif; font-size: 7.5pt; line-height: 16px;" class="">
<span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">UNIVERSITÉ DU LUXEMBOURG</span><br class="">
<span style="display: inline;" class=""><br class="">
</span><span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">LUXEMBOURG CENTRE FOR SYSTEMS BIOMEIDINCE</span><br class="">
<span style="color: rgb(61, 59, 59); display: inline;" class="">Campus Belval | House of Biomedicine
<br class="">
7, avenue des Hauts-Fourneaux <br class="">
L-4362 Esch-sur-Alzette </span><br class="">
<span style="color: rgb(61, 59, 59); display: inline;" class="">T: </span><span style="color: rgb(61, 59, 59); display: inline;" class="">+352 46 66 44 6124</span>
<br class="">
<span style="color: rgb(61, 59, 59); display: inline;" class="">F: </span><span style="color: rgb(61, 59, 59); display: inline;" class="">+352 46 66 44 6949</span>
<span style="display: inline;" class=""><br class="">
</span><a href="http://www.uni.lu/lcsb" style="color: rgb(0, 109, 189); display: inline;" class="">http://www.uni.lu/lcsb</a>
</p>
<p style="font-family: Arial, sans-serif; font-size: 14px; line-height: 16px;" class="">
<a href="https://www.facebook.com/trefex" style="display: inline;" class=""><img width="24" height="24" data-filename="facebook.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/facebook.png" alt="Facebook" class=""></a>
<a href="https://twitter.com/Trefex" style="display: inline;" class=""><img width="24" height="24" data-filename="twitter.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/twitter.png" alt="Twitter" class=""></a>
<a href="https://plus.google.com/+ChristopheTrefois/" style="display: inline;" class="">
<img width="24" height="24" data-filename="googleplus.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/googleplus.png" alt="Google Plus" class=""></a>
<a href="https://www.linkedin.com/in/trefoischristophe" style="display: inline;" class="">
<img width="24" height="24" data-filename="linkedin.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/linkedin.png" alt="Linkedin" class=""></a>
<a href="http://skype:Trefex?call" style="display: inline;" class=""><img width="24" height="24" data-filename="skype.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/skype.png" alt="skype" class=""></a>
</p>
<div style="font-family: Arial, sans-serif; font-size: 14px; line-height: 16px;" class="">
<br class="webkit-block-placeholder">
</div>
<p style="font-family: Arial, sans-serif; color: rgb(61, 59, 59); font-size: 9px; line-height: 16px;" class="">
----<br class="">
This message is confidential and may contain privileged information. <br class="">
It is intended for the named recipient only. <br class="">
If you receive it in error please notify me and permanently delete the original message and any copies.
<br class="">
----<br class="">
</p>
</div>
<br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 09 Feb 2015, at 12:31, Sebastien Besson (Staff) <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><br class="">
The University of Dundee is a registered Scottish Charity, No: SC015096<br class="">
<br class="">
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class="">
<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">From:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">"Sebastien Besson (Staff)" <<a href="mailto:s.besson@dundee.ac.uk" class="">s.besson@dundee.ac.uk</a>><br class="">
</span></div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class="">
<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">To:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">OME-devel OME <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a>><br class="">
</span></div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class="">
<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Subject:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class=""><b class="">Re: [ome-devel] Hypercube out of memory</b><br class="">
</span></div>
<div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;" class="">
<span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif; color:rgba(127, 127, 127, 1.0);" class=""><b class="">Date:
</b></span><span style="font-family: -webkit-system-font, Helvetica Neue, Helvetica, sans-serif;" class="">9 Feb 2015 12:31:46 CET<br class="">
</span></div>
<br class="">
<br class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Christophe,
<div class=""><br class="">
</div>
<div class="">you should be abele to set any value for MessageSizeMax via an ice.config file.</div>
<div class=""><br class="">
</div>
<div class="">See the corresponding line in the ice.config file included in the OMERO.matlab:</div>
<div class=""><a href="https://github.com/openmicroscopy/openmicroscopy/blob/v.5.0.7/etc/ice.config#L123" class="">https://github.com/openmicroscopy/openmicroscopy/blob/v.5.0.7/etc/ice.config#L123</a></div>
<div class=""><br class="">
</div>
<div class="">Let us know if this does not work,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
<div class="">
<div class="">On 9 Feb 2015, at 11:14, Christophe TREFOIS <<a href="mailto:christophe.trefois@uni.lu" class="">christophe.trefois@uni.lu</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Dear all,
<div class=""><br class="">
</div>
<div class="">I tried the example in the OMERO Matlab doc to load a hypercube from a 1GB tiff file</div>
<div class=""><br class="">
</div>
<div class="">I used the following tutorial: <a href="http://www.openmicroscopy.org/site/support/omero5/developers/Matlab.html" class="">http://www.openmicroscopy.org/site/support/omero5/developers/Matlab.html</a></div>
<div class=""><br class="">
</div>
<div class="">I get the following error when trying to “getHypercube”</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">Java exception occurred:</div>
<div class="">Ice.UnknownLocalException</div>
<div class=""> unknown = "Ice::MemoryLimitException</div>
<div class=""> Ice.MemoryLimitException</div>
<div class=""> reason = "requested 1424673822 bytes, maximum allowed is 67108864 bytes (see Ice.MessageSizeMax)”</div>
<div class=""><br class="">
</div>
<div class="">Is it possible to increase the MessageSizeMax or is it not advised and if so, how could I load my hypercube into Matlab anyway?</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">
<meta name="format-detection" content="telephone=no" class="">
<p style="font-family: Arial, sans-serif; font-size: 10pt; line-height: 16px; color: rgb(33, 33, 33);" class="">
<span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">Dr Christophe Trefois, Dipl.-Ing.</span>
<span style="display: inline;" class=""></span><br class="">
<span style="color: rgb(61, 59, 59); display: inline; font-size:7.5pt;" class="">Technical Specialist / Post-Doc</span>
</p>
<p style="font-family: Arial, sans-serif; font-size: 7.5pt; line-height: 16px;" class="">
<span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">UNIVERSITÉ DU LUXEMBOURG</span><br class="">
<span style="display: inline;" class=""><br class="">
</span><span style="font-weight: bold; color: rgb(61, 59, 59); display: inline;" class="">LUXEMBOURG CENTRE FOR SYSTEMS BIOMEIDINCE</span><br class="">
<span style="color: rgb(61, 59, 59); display: inline;" class="">Campus Belval | House of Biomedicine
<br class="">
7, avenue des Hauts-Fourneaux <br class="">
L-4362 Esch-sur-Alzette </span><br class="">
<span style="color: rgb(61, 59, 59); display: inline;" class="">T: </span><span style="color: rgb(61, 59, 59); display: inline;" class="">+352 46 66 44 6124</span>
<br class="">
<span style="color: rgb(61, 59, 59); display: inline;" class="">F: </span><span style="color: rgb(61, 59, 59); display: inline;" class="">+352 46 66 44 6949</span>
<span style="display: inline;" class=""><br class="">
</span><a href="http://www.uni.lu/lcsb" style="color: rgb(0, 109, 189); display: inline;" class="">http://www.uni.lu/lcsb</a>
</p>
<p style="font-family: Arial, sans-serif; font-size: 14px; line-height: 16px;" class="">
<a href="https://www.facebook.com/trefex" style="display: inline;" class=""><img width="24" height="24" data-filename="facebook.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/facebook.png" alt="Facebook" class=""></a>
<a href="https://twitter.com/Trefex" style="display: inline;" class=""><img width="24" height="24" data-filename="twitter.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/twitter.png" alt="Twitter" class=""></a>
<a href="https://plus.google.com/+ChristopheTrefois/" style="display: inline;" class="">
<img width="24" height="24" data-filename="googleplus.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/googleplus.png" alt="Google Plus" class=""></a>
<a href="https://www.linkedin.com/in/trefoischristophe" style="display: inline;" class="">
<img width="24" height="24" data-filename="linkedin.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/linkedin.png" alt="Linkedin" class=""></a>
<a href="http://skype:Trefex?call" style="display: inline;" class=""><img width="24" height="24" data-filename="skype.png" src="https://s3.amazonaws.com/htmlsig-assets/rounded/skype.png" alt="skype" class=""></a>
</p>
<div style="font-family: Arial, sans-serif; font-size: 14px; line-height: 16px;" class="">
<br class="webkit-block-placeholder">
</div>
<p style="font-family: Arial, sans-serif; color: rgb(61, 59, 59); font-size: 9px; line-height: 16px;" class="">
----<br class="">
This message is confidential and may contain privileged information. <br class="">
It is intended for the named recipient only. <br class="">
If you receive it in error please notify me and permanently delete the original message and any copies.
<br class="">
----<br class="">
</p>
</div>
<br class="">
</div>
</div>
_______________________________________________<br class="">
ome-devel mailing list<br class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br class="">
</blockquote>
</div>
<br class="">
<div class=""><span class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class="">
<span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; border-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-stroke-width: 0px;">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; " class="">
<div class="">Dr Sébastien Besson</div>
<div class="">Open Microscopy Environment / Harvard Medical School</div>
<div class="">Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div class="">College of Life Sciences, University of Dundee, Dow Street,</div>
<div class="">Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
</div>
</span></div>
</span></div>
<br class="">
</div>
</div>
<br class="">
<br class="">
_______________________________________________<br class="">
ome-devel mailing list<br class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
_______________________________________________<br class="">
ome-devel mailing list<br class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
</div>
_______________________________________________<br>
ome-devel mailing list<br>
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><br>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel<br>
</blockquote>
</div>
<br>
</div>
</div>
<br>
<br>
<div><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<div>Dr Sébastien Besson</div>
<div>Open Microscopy Environment / Harvard Medical School</div>
<div>Wellcome Trust Centre for Gene Regulation and Expression,</div>
<div>College of Life Sciences, University of Dundee, Dow Street,</div>
<div>Dundee DD1 5EH Scotland UK Tel: (01382) 386364</div>
</div>
</span></div>
</span></span></div>
<br>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</body>
</html>